Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22.34 kDa 
• Atom Count: 1694 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

3TTP

Structure of multiresistant HIV-1 protease in complex with darunavir

• PDB DOI: 10.2210/pdb3TTP/pdb

• Classification: Hydrolase/hydrolase inhibitor
• Organism(s): Human immunodeficiency virus type 1 (BRU ISOLATE)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-09-15 Released: 2012-09-26 
• Deposition Author(s): Saskova, K.G., Brynda, J., Kozisek, M., Konvalinka, J., Rezacova, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.265 
• R-Value Work: 0.197 
• R-Value Observed: 0.200 

Literature

Thermodynamic and structural analysis of HIV protease resistance to darunavir - analysis of heavily mutated patient-derived HIV-1 proteases.

Kozisek, M., Lepsik, M., Grantz Saskova, K., Brynda, J., Konvalinka, J., Rezacova, P.

(2014) FEBS J 281: 1834-1847

• PubMed: 24785545 
• DOI: 10.1111/febs.12743
• Primary Citation of Related Structures:  
  3TTP, 4LL3


• PubMed Abstract: 
  

We report enzymologic, thermodynamic and structural analyses of a series of six clinically derived mutant HIV proteases (PR) resistant to darunavir. As many as 20 mutations in the resistant PRs decreased the binding affinity of darunavir by up to 13 000-fold, mostly because of a less favorable enthalpy of binding that was only partially compensated by the entropic contribution. X-ray structure analysis suggested that the drop in enthalpy of darunavir binding to resistant PR species was mostly the result of a decrease in the number of hydrogen bonds and a loosening of the fit between the inhibitor and the mutated enzymes. The favorable entropic contribution to darunavir binding to mutated PR variants correlated with a larger burial of the nonpolar solvent-accessible surface area upon inhibitor binding. We show that even very dramatic changes in the PR sequence leading to the loss of hydrogen bonds with the inhibitor could be partially compensated by the entropy contribution as a result of the burial of the larger nonpolar surface area of the mutated HIV PRs.

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Organizational Affiliation: 

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Prague, Czech Republic.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 protease	A, B	99	Human immunodeficiency virus type 1 (BRU ISOLATE)	Mutation(s): 20  Gene Names: gag-pol EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)) Explore P03367  Go to UniProtKB:  P03367

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
017	C [auth A]	(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE C27 H37 N3 O7 S CJBJHOAVZSMMDJ-HEXNFIEUSA-N
BME	E [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
CL	D [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.265 
• R-Value Work: 0.197 
• R-Value Observed: 0.200 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.66	α = 90
b = 61.66	β = 90
c = 83.07	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-09-15 
• Released Date: 2012-09-26 
Deposition Author(s): Saskova, K.G., Brynda, J., Kozisek, M., Konvalinka, J., Rezacova, P.

Revision History  

• Version 1.0: 2012-09-26
  Type: Initial release
  
• Version 1.1: 2014-04-16
  Changes: Database references
• Version 1.2: 2014-06-11
  Changes: Database references
• Version 1.3: 2020-02-26
  Changes: Data collection, Database references